15:02:04 <RRSAgent> RRSAgent has joined #hcls
15:02:04 <RRSAgent> logging to http://www.w3.org/2012/10/09-hcls-irc
15:02:33 <Zakim> +mscottm
15:02:35 <Zakim> + +1.206.732.aabb
15:02:56 <michel> michel has joined #hcls
15:03:03 <Zakim> +michel
15:04:02 <mscottm> Zakim, +1.206.732.aabb is Michael
15:04:02 <Zakim> +Michael; got it
15:04:11 <Zakim> +EricP
15:04:23 <mscottm> Zakim, +1.414.955.aaaa is Tomasz
15:04:23 <Zakim> +Tomasz; got it
15:06:05 <Tomasz> Erik, how do you define Mapped Data?
15:07:49 <michael> michael has joined #HCLS
15:08:10 <Zakim> + +44.122.383.aacc
15:08:50 <mscottm> https://groups.google.com/forum/?fromgroups=#!topic/expressionrdf/j5I8Tqwr3Dc
15:09:54 <Zakim> + +44.785.552.aadd
15:10:07 <mscottm> https://docs.google.com/drawings/d/1ZFA72YBEcc6BQp31GsAJI1L6WK0mPuNltIkpp8WMcSk/edit
15:10:38 <mscottm> Zakim, +44.785.552.aadd is Simon
15:10:38 <Zakim> +Simon; got it
15:11:20 <James> James has joined #HCLS
15:12:13 <mscottm> Zakim, +44.122.383.aacc is James
15:12:13 <Zakim> +James; got it
15:12:54 <Zakim> +[IPcaller]
15:13:48 <jupp> jupp has joined #HCLS
15:13:50 <mscottm> Zakim, +[IPcaller] is Chisato
15:13:50 <Zakim> sorry, mscottm, I do not recognize a party named '+[IPcaller]'
15:14:03 <mscottm> Zakim, [IPcaller] is Chisato
15:14:03 <Zakim> +Chisato; got it
15:14:20 <mscottm> Zakim, Simon is jupp
15:14:20 <Zakim> +jupp; got it
15:15:01 <mscottm> https://docs.google.com/drawings/d/1ZFA72YBEcc6BQp31GsAJI1L6WK0mPuNltIkpp8WMcSk/edit
15:20:36 <ericP> michel, do you have an SVG of this image?
15:20:52 <michel> Basic idea is that experiments are composed of a number of steps (e.g. sample preparation, bioassay, data processing) each of which have inputs and outputs
15:21:13 <ericP> i'd like to play with it a bit to change the direction and label of the has_input arcs so you can visually see a data flow
15:21:27 <michel> you can save it as svg
15:22:59 <James> in general output is used to model processes and things they produce
15:23:05 <James> has_output that is
15:23:08 <ericP> authoritative version is google?
15:24:54 <James> what type of thing is experiment michel?
15:26:35 <mscottm> SIO diagram (refines last one) https://docs.google.com/drawings/d/1pn86hwXfF87oz2tQr2r5pb95CB_Q-kmCMe2AGs3dxHw/edit
15:27:25 <michel> james -> an experimetn is a process
15:28:50 <James> ok tnx
15:28:58 <jupp> http://wwwdev.ebi.ac.uk/fgpt/efosemweb.html
15:30:25 <James> so every gene list is generared using pairwise comparisons
15:32:19 <jupp> http://www.ebi.ac.uk/gxa/experiment/E-GEOD-1659
15:34:37 <James> the other thing to say is that this will change with the new stats for atlas
15:34:43 <ericP> michel, what's the relationship between "has input" and "is source of" (latter connecting "test sample" and "gene expression value" to "test-control differential gene expression value"
15:34:47 <ericP> )
15:36:44 <michel> 'has input' is between a process and an object
15:37:08 <ericP> ahh, it runs through "gene expression value", but the the actual terminus is the "control sample"
15:37:09 <michel> 'is source of' is between an object to another object
15:37:17 <michael> q-value: A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant.  To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level.
15:38:51 <James> i'd agree michel - we're sold on the pattern
15:49:31 <ericP> created a multi-color version of michel's figure: https://docs.google.com/drawings/d/1xIvQzFPWYbioqs-k9-u8veP7zmW1_b6RRFE1FMbKS1Q/edit
15:49:35 <ericP> in an effort to track the flow of material and data, i reversed some arrows and changed their labels: s/has input/input for/  and  s/is derived from/material for/
15:50:15 <ericP> of course, this favors user comprehension over accurately conveying the ontology
15:50:25 <mscottm> https://docs.google.com/document/d/1A5-3tOsifPWPpETBKU-ZA9d7O7wK_nBzTFUBEe-0Bzo/edit?authkey=CK-y8Y8C&authkey=CK-y8Y8C#
15:51:11 <mscottm> expression RDF note draft: https://docs.google.com/document/d/1A5-3tOsifPWPpETBKU-ZA9d7O7wK_nBzTFUBEe-0Bzo/edit?authkey=CK-y8Y8C&authkey=CK-y8Y8C#
15:52:00 <ericP> michael, it's left as an exercise for the reader
15:52:05 <ericP> like fermat's last theorum
15:54:20 <ericP> michel, (noting that you are viewing the image i created) should the material channel (the blue at the bottom) be a different color from the process channel?
15:54:24 <ericP> like maybe blood red?
16:02:11 <James> sorry i have to run as have call at 5
16:02:37 <Zakim> -James
16:11:26 <Zakim> -EricP
16:11:47 <Zakim> -Michael
16:11:48 <Zakim> -Tomasz
16:11:50 <Zakim> -jupp
16:11:51 <Zakim> -michel
16:11:53 <Zakim> -mscottm
16:12:03 <Zakim> -Chisato
16:12:04 <Zakim> SW_HCLS()11:00AM has ended
16:12:04 <Zakim> Attendees were mscottm, michel, Michael, EricP, Tomasz, James, Chisato, jupp
16:21:42 <mscottm> mscottm has joined #hcls
16:21:47 <mscottm> Zakim, please generate minutes
16:21:47 <Zakim> I don't understand 'please generate minutes', mscottm
16:22:44 <mscottm> RRSAgent, draft minutes
16:22:44 <RRSAgent> I have made the request to generate http://www.w3.org/2012/10/09-hcls-minutes.html mscottm
16:23:44 <mscottm> [michel, all]Discussion of cleaning up tables of key concepts and their mappings.
16:24:49 <mscottm> michel: <proposes new demo that employs OWL mappings analog of SWObjects> 
16:25:20 <mscottm> Scott: wary of adding new items before shipping the note
16:25:30 <mscottm> Eric: You can always version it.
16:26:29 <mscottm> Scott: Would prefer to version it. Time is right to publish what we've discussed. But maybe it's possible to put the demo together by the time the rest of the doc is ready.
16:26:45 <mscottm> Michel: What will the note look like?
16:27:59 <mscottm> Scott: The way it does now + rewrite + some of the GXA specifics that have recently been settled.
16:28:16 <mscottm> RRSAgent, draft minutes
16:28:16 <RRSAgent> I have made the request to generate http://www.w3.org/2012/10/09-hcls-minutes.html mscottm
16:28:23 <mscottm> rrsagent, make log world-visible
17:04:07 <mscottm> mscottm has joined #hcls
18:33:34 <egonw__> egonw__ has joined #HCLS
18:38:17 <Zakim> Zakim has left #hcls